Evaluate gene sets identified by SDAN
Wei Sun
2024-07-10
Setup
Check enrichment of gene sets
Read in gene info and gene set assignments
file_tag = sprintf("%s_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 32.00 35.00 37.00 36.30 37.25 40.00## [1] 40## [1] 32 32 32 33 33 33 34 34 35 35 35 36 36 36 36 36 37 37 37 37 37 37 37 37 37
## [26] 37 37 37 37 37 38 38 38 38 38 38 38 40 40 40Find gene symbols
Find gene symbols from bioMart.
All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]Find gene symbols using the alias2Symbol function from
limma.
a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "MPP6"
## [1] "MPHOSPH6" "PALS2"##
## FALSE TRUE
## 1643 357##
## FALSE TRUE <NA>
## 21 1622 357gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: BTBD11 ABTB3
## 2: LINC01006 RNF32-DT
## 3: LINC01185 REL-DT
## 4: ZRANB2-AS2 ZRANB2-DT
## 5: LINC00271 AHI1-DT
## 6: RFX3-AS1 RFX3-DT
## 7: COX10-AS1 COX10-DT
## 8: SUCLG2-AS1 SUCLG2-DT
## 9: C5orf17 LINC02899
## 10: OSMR-AS1 OSMR-DT
## 11: C8orf37-AS1 CFAP418-AS1
## 12: CTB-178M22.2 TENM2-AS1
## 13: LINC00637 PPP1R13B-DT
## 14: MPP6 MPHOSPH6
## 15: C7orf61 SPACDR
## 16: C3orf35 APRG1
## 17: HRAT92 PDGFA-DT
## 18: LINC00884 ATP13A3-DT
## 19: LINC01137 ZC3H12A-DT
## 20: TMEM161B-AS1 TMEM161B-DT
## 21: MAFG-DT MILIP
## sym_in_data sym_limmagene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")),
gene_symbol := sym_limma]
dim(gene_info)## [1] 2000 3## sym_in_data sym_limma gene_symbol
## 1: CD38 CD38 CD38
## 2: PRKAR2B PRKAR2B PRKAR2B
## 3: ASB4 ASB4 ASB4
## 4: USH1C USH1C USH1C
## 5: ARHGAP44 ARHGAP44 ARHGAP44## t1
## 1
## 2000Prepare gene set information
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp"## reactome go_bp
## 1692 7647Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0Conduct enrichment analysis
## [1] 2000 3## sym_in_data sym_limma gene_symbol
## 1: CD38 CD38 CD38
## 2: PRKAR2B PRKAR2B PRKAR2B## [1] 36517 9## gene_ids feature_is_filtered feature_name feature_reference
## 1: ENSG00000000003 FALSE TSPAN6 NCBITaxon:9606
## 2: ENSG00000000005 FALSE TNMD NCBITaxon:9606
## feature_biotype n_cells_by_counts mean_counts pct_dropout_by_counts
## 1: gene 6900 0.118699020 90.14412
## 2: gene 161 0.002485395 99.77003
## total_counts
## 1: 8310
## 2: 174## [1] 2000##
## TRUE
## 2000##
## FALSE TRUE
## 34517 2000gene_dat$selected = 0
gene_dat$selected[match(gene_info$sym_in_data, gene_dat$feature_name)] = 1
table(gene_dat$selected)##
## 0 1
## 34517 2000## $`0`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00857 90.44551 99.20296 90.72478 99.93429 100.00000
##
## $`1`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00 60.04 81.87 72.81 92.88 97.99gene_info = merge(gene_info, gene_dat, by.x="sym_in_data",
by.y="feature_name", all.x = TRUE, all.y = FALSE)
dim(gene_info)## [1] 2000 12## sym_in_data sym_limma gene_symbol gene_ids feature_is_filtered
## 1: A2M A2M A2M ENSG00000175899 FALSE
## 2: A2ML1-AS1 A2ML1-AS1 A2ML1-AS1 ENSG00000256661 FALSE
## feature_reference feature_biotype n_cells_by_counts mean_counts
## 1: NCBITaxon:9606 gene 5826 0.1207987
## 2: NCBITaxon:9606 gene 11030 0.2138297
## pct_dropout_by_counts total_counts selected
## 1: 91.67821 8457 1
## 2: 84.24488 14970 1max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol",
bias.data = 100 - gene_info$pct_dropout_by_counts)
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.05)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=81)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "PRKAR2B" "NRXN3" "ELAVL2" "MMP16" "CADPS"
## [6] "CCSER1" "SYT1" "MAP2" "RBFOX1" "PDE1A"
## [11] "RIMS3" "DPP6" "LRRC4B" "SNTG1" "CACNA1B"
## [16] "RBFOX3" "GRM5" "NLGN1" "FRMPD4" "DLGAP1"
## [21] "ARPP21" "CNTNAP2" "RIMS2" "CSMD1" "OPCML"
## [26] "KCNH7" "RALYL" "SYN3" "KCNIP4" "ELAVL3"
## [31] "RYR2" "MEG3" "RP1-30E17.2" "IQCJ-SCHIP1"
## [1] 2
## [1] "SLC26A3" "STEAP1B" "TFCP2L1"
## [4] "ZSWIM4" "NKD1" "CCDC3"
## [7] "ESYT3" "SYTL3" "SEMA3E"
## [10] "SLC26A5" "FRMD3" "RTN4RL1"
## [13] "PLK5" "NWD1" "AC023469.1"
## [16] "AC003991.3" "AC104088.1" "AC002127.4"
## [19] "RP11-154D17.1" "EPCAM-DT" "RP11-384F7.1"
## [22] "ALDH1L1-AS2" "RP11-17A1.3" "RP11-26J3.1"
## [25] "RP11-20D14.3" "RP11-507B12.2" "CASC17"
## [28] "CEACAM16-AS1" "MIR23AHG" "CTD-2189E23.1"
## [31] "RMRP_ENSG00000269900" "SPANXA2-OT1" "RP11-154H23.4"
## [34] "RP11-596C23.6" "RP4-799O8.1" "RP11-465L10.14"
## [37] "RP3-466I7.2"
## [1] 3
## [1] "PSD" "SEZ6L" "SLC2A9" "ST6GALNAC5"
## [5] "KIRREL3" "MAP3K7CL" "SYNPR" "NDST3"
## [9] "GRIK2" "METTL2B" "NEGR1" "CALN1"
## [13] "SGCZ" "SLIT1" "ERC2" "DLGAP2"
## [17] "FBXO16" "RP11-170M17.1" "AC011288.2" "LINC01503"
## [21] "MSC-AS1" "RP11-20I20.2" "RP11-586K2.1" "RP4-809F18.1"
## [25] "PWRN1" "GEMIN7-AS1" "SYNPO2L-AS1" "RP11-640F22.1"
## [29] "RP11-320L2.1" "CLIP2" "TGIF2" "UNC13C"
## [33] "SLC6A9" "AJAP1" "ODAD4" "KRTAP5-AS1"
## [1] 4
## [1] "WARS1" "HDAC9"
## [3] "CDON" "TMEM38A"
## [5] "ITPKC" "CATSPERG"
## [7] "CDKL1" "PADI2"
## [9] "KLHL29" "RAP1GAP2"
## [11] "TMTC1" "KIAA0513"
## [13] "SLC44A5" "CBLN2"
## [15] "BOC" "SEC24D"
## [17] "ZNF385D" "ST3GAL2"
## [19] "FBXO27" "EDIL3"
## [21] "GPR176" "ATOH8"
## [23] "GPR137C" "SPATA13_ENSG00000182957"
## [25] "ZBTB7C" "CACNA1E"
## [27] "MEF2B" "RP11-191L9.4"
## [29] "RP11-513I15.6" "NRSN2-AS1"
## [31] "LINC00685" "RP5-864K19.4"
## [33] "RP11-147G16.1" "CTC-340A15.2"
## [35] "RP11-79E3.2" "DGCR5_ENSG00000273032"
## [37] "CASTOR2"
## [1] 5
## [1] "LRRC7" "PON3" "PLAGL1" "MAEL"
## [5] "SLC9B1" "SCN11A" "FSTL5" "CATSPERE"
## [9] "COL5A2" "AC012593.1" "ZRANB2-AS2" "MIR181A1HG"
## [13] "LINC01036" "RAP2C-AS1" "UFL1-AS1" "PPP1R9A-AS1"
## [17] "RP11-4B14.3" "PTPRG-AS1" "RP11-167H9.4" "H2AZ1-DT"
## [21] "RP11-461O7.1" "LINC00504" "LINC02144" "CTB-161M19.4"
## [25] "RP11-380P13.1" "C8orf37-AS1" "AB015752.3" "LINC02740"
## [29] "RP11-260G13.1" "RP11-525K10.3" "ADGRL1-AS1" "RP11-103J8.1"
## [33] "RP11-964E11.3" "RP4-681L3.3" "RP4-660H19.2" "RP1-84D21.2"
## [37] "RP11-120J1.2" "C1orf87"
## [1] 6
## [1] "SP140" "SEL1L2" "ANKRD7" "PAPPA2"
## [5] "RGS22" "SAXO1" "MEGF11" "PKD1L1"
## [9] "SPATA17" "OTOGL" "ODAD2" "GPR39"
## [13] "ENO4" "SCOC-AS1" "LEKR1" "LINC01876"
## [17] "RP11-162D16.2" "LINC01277" "AC079807.4" "LINC00271"
## [21] "RP11-154D6.1" "LINC01358" "RP11-446H18.5" "LINC01340"
## [25] "LINC00534" "CTB-178M22.2" "RP11-727A23.10" "LINC02745"
## [29] "RP11-352M15.1" "LINC02320" "SPESP1" "RP11-524F11.2"
## [33] "LINC00907" "LINC00506" "RP11-444C24.1" "RP11-335E8.3"
## [37] "AC064875.2" "TSBP1-AS1"
## [1] 7
## [1] "ASB4" "HSD11B1" "PLK2" "ZCCHC18" "SP140L" "KCNG1"
## [7] "SYNE2" "CDH3" "NGEF" "ZFY" "RASGRP2" "ARHGAP15"
## [13] "ANGPT2" "PCDH11Y" "NAMPT" "ARID3A" "TNNT2" "KIAA1217"
## [19] "HS3ST2" "AIF1L" "C1QL1" "SLC6A6" "ANXA1" "SRRM4"
## [25] "RIT2" "FBXO32" "CATIP" "SPATA2L" "ITGA5" "REPS2"
## [31] "VAT1L" "NXNL1" "PCP4" "POTEG" "AFAP1" "STARD10"
## [1] 8
## [1] "MT3" "EPM2A" "ACAT2" "GFRA1" "GRIA4" "DLC1" "ANO5"
## [8] "PTPRN" "PIR" "DOK5" "GLIS3" "B4GALT2" "MACF1" "NCAN"
## [15] "NAV1" "CCNH" "SOX5" "HAVCR2" "TMOD1" "SSH2" "TIAM2"
## [22] "CNNM2" "ABR" "SPTBN4" "OXR1" "FAT3" "SLC20A2" "CRADD"
## [29] "PFKFB3" "FRMD5" "MYO1D" "SAMD12" "KCNQ5" "WWOX" "S100A10"
## [36] "EML6"
## [1] 9
## [1] "TESC" "P3H2" "CHRNE" "WASF1" "IL1R1"
## [6] "HELB" "TICAM1" "GALNT8" "PTPRE" "TTC9"
## [11] "IRAK2" "TTLL7" "AK7" "ITPRIP" "ADAM12"
## [16] "PLCL2" "LRGUK" "CFAP161" "CFAP251" "ORAI2"
## [21] "TMCO4" "SHISA5" "NFIL3" "TMC1" "DEPP1"
## [26] "COL24A1" "PRIMA1" "TSHZ2" "MAFF" "OVCH1"
## [31] "RASGEF1A" "NHSL2" "TCEA3" "MIR34AHG" "SATB1-AS1"
## [36] "RP11-403A3.3"
## [1] 10
## [1] "CEMIP" "COL4A2" "UNC5D" "SGCD"
## [5] "MACROD2" "RNLS" "RP11-111A21.1" "RP11-692P14.1"
## [9] "PLXNA2" "SYT17" "COBL" "LGI1"
## [13] "PRR12" "HIP1" "ZSWIM6" "MAPK4"
## [17] "SDK1" "FAM13C" "THRB" "RHPN1"
## [21] "AHCYL2" "RFTN2" "FAM107A" "FAXDC2"
## [25] "FAM222B" "SYT12" "IQCK" "FIGN"
## [29] "SLC25A18" "LHFPL6" "FLRT2" "DMWD"
## [33] "ARHGEF26-AS1" "STX18-AS1" "AGBL1"
## [1] 11
## [1] "EFCAB11" "C11orf65" "DNAH12" "LINC01006"
## [5] "RHCE" "HMGN5" "CRPPA" "AC105760.2"
## [9] "LINC01185" "AC008269.2" "LINC01239" "RP1-230L10.1"
## [13] "NECTIN3-AS1" "RP11-550I24.2" "RP11-436F23.1" "LINC02196"
## [17] "LINC02615" "CTC-347C20.1" "LINC02326" "RP11-16B13.1"
## [21] "IDH2-DT" "CRTC3-AS1" "AC004158.3" "PLS3-AS1"
## [25] "LINC02664" "CTC-428H11.2" "CTD-2313D3.2" "RP11-788A4.3"
## [29] "RP11-168F16.1" "LMNTD1" "TVP23A" "GSG1L"
## [33] "TOGARAM2" "AP000318.2" "RP11-348F1.3" "RP11-190P13.2"
## [37] "RP11-148E17.1" "RP11-210M15.2"
## [1] 12
## [1] "RNF175" "RETREG1" "GPC6" "GRM7"
## [5] "SYT7" "ATP9A" "FRY" "RASL12"
## [9] "ATRNL1" "ABCC3" "MAN1C1" "GFPT2"
## [13] "SCN2A" "SCN1A" "SLC4A10" "ZNF385B"
## [17] "CDH18" "CNTN5" "SLC24A2" "MYO1E"
## [21] "NFASC" "PGM2L1" "KIF5C" "TPST1"
## [25] "SLCO3A1" "SLC8A1" "PDE2A" "SHTN1"
## [29] "NHS" "PTPRT" "LINC00632" "TNFRSF25"
## [33] "AC067956.1" "SHISA9" "PTCHD4" "LINC01411"
## [37] "LINC02506" "RP11-624C23.1"
## [1] 13
## [1] "IL7" "MT1G" "APOE" "CCDC59"
## [5] "PDE5A" "SYCP2L" "GLRX" "PLD5"
## [9] "PROS1" "EYS" "HES4" "F5"
## [13] "LUCAT1" "RP11-624D11.2" "LINC02389" "GAS7"
## [17] "RHOBTB1" "KNOP1" "TSHZ3" "HIVEP3"
## [21] "DIAPH2" "PXDNL" "ART3" "SLC5A11"
## [25] "PDPN" "ABCA1" "LINGO1" "DPYD"
## [29] "TMEM229B" "MMP17" "LINC01320" "LINC01322"
## [1] 14
## [1] "CPED1" "SPATA6L" "F3" "SLC14A1"
## [5] "SLC44A3" "SLC22A3" "SLC43A2" "FTH1"
## [9] "ERICH3" "CCBE1" "WNT7B" "MAMDC2-AS1"
## [13] "MALRD1" "SOX1-OT" "CHL1-AS2" "PPP1R26-AS1"
## [17] "XIST" "OBI1-AS1" "LINC01934" "RP11-390F4.6"
## [21] "SUCLG2-AS1" "BAALC-AS1" "LINC01182" "LINC00923"
## [25] "LINC00499" "GS1-57L11.1" "RP11-156K13.1" "RMST"
## [29] "RP11-798K3.2" "AC007193.6" "RP11-496B10.6" "RP11-382N13.7"
## [33] "RP11-563M4.2"
## [1] 15
## [1] "XK" "BCAS1" "PCSK1N" "SRPX2"
## [5] "CALY" "CHST9" "CHODL" "FREM1"
## [9] "VWA3A" "NPSR1-AS1" "TSBP1" "MT1H"
## [13] "RNF212B" "RP4-660H19.1" "RP11-735G4.1" "RP11-106M7.1"
## [17] "RP11-141A19.1" "DPP10-AS3" "DIRC3" "LINC01524"
## [21] "DPP10-AS1" "RP11-475C16.2" "RP11-624M8.1" "LINC02877"
## [25] "PRKAR2B-AS1" "LINC02355" "RP11-114J13.1" "RP11-711G10.1"
## [29] "LINC02715" "MAP1LC3B2" "LINC01579" "DIO2-AS1"
## [33] "RP11-80I3.1" "RP11-290O12.2" "SLC7A14-AS1" "RP11-725F23.1"
## [37] "RP11-875G18.1" "RP5-892C22.1"
## [1] 16
## [1] "PUDP" "ADRA1B" "LRRC3B" "EPS15-AS1"
## [5] "RP11-134O21.1" "RP11-242P2.1" "CH17-174L20.1" "CTD-2126E3.6"
## [9] "RP11-624A4.2" "WFDC1" "XYLT1" "CPEB3"
## [13] "RIPOR2" "DMGDH" "LGR6" "KCNJ16"
## [17] "PID1" "GNA14" "MRAS" "PTCHD1"
## [21] "CHST11" "LRRC8C" "HPSE2" "FZD8"
## [25] "CTD-2527I21.15" "LDLRAD3" "NME9" "TMEM184B"
## [29] "PLIN5" "LINC00511" "HPN-AS1" "PTCHD1-AS"
## [33] "AC016745.3" "LINC02208" "RP11-237N2.1" "RP11-183J19.1"
## [37] "RP11-404C6.6"
## [1] 17
## [1] "USH1C" "DNAH9" "SLC39A14" "CAP2" "PHACTR2"
## [6] "UBE3D" "ELL2" "MGAT3" "CA3" "LRRN2"
## [11] "GPR156" "C9orf153" "RP1-223B1.1" "TRMT9B" "CD99"
## [16] "KLF6" "AEBP1" "SUFU" "ZFP36" "QRICH2"
## [21] "ZBTB46" "RFTN1" "GMPR" "EGF" "GABPB2"
## [26] "ZNF208" "WNK2" "LDLRAD4" "IFFO2" "SYNM"
## [31] "RGS6" "ZNF594-DT"
## [1] 18
## [1] "IDI1" "DPH6" "FADS2" "C2CD6"
## [5] "ALDH1A1" "PAH" "CYP7B1" "CASC2"
## [9] "COL25A1" "CC2D2B" "DCHS2" "FIRRE"
## [13] "AC004540.5" "COL28A1" "POT1-AS1" "LYPLAL1-DT"
## [17] "LINC01344" "AC007682.1" "RFX3-AS1" "COX10-AS1"
## [21] "LINC01376" "AC079305.11" "RNF217-AS1" "RP11-268P4.5"
## [25] "RP11-284M14.1" "RP11-679C8.2" "RP11-582J16.4" "RP11-404I7.2"
## [29] "RP11-673E1.1" "ZFHX4-AS1" "RP11-157I4.4" "RP11-541P9.3"
## [33] "MPPED2-AS1" "RP11-511B23.2" "LINC02328" "CTC-498M16.4"
## [37] "RP3-383B8.1" "CTD-2297M2.1"
## [1] 19
## [1] "BAIAP3" "USH2A" "FAP" "KLF2"
## [5] "RHBDL3" "FAM151B" "GAL3ST2" "DRC1"
## [9] "LRRC2" "NPNT" "NOTUM" "PAX8-AS1"
## [13] "LAMA2" "C3orf35" "LINC00862" "CFI"
## [17] "RP11-174G6.1" "AC003090.1" "RP11-69I8.3" "RP1-35C21.2"
## [21] "CYP1B1-AS1" "LINC01137" "IQCM" "L3MBTL2-AS1"
## [25] "RP11-279O9.4" "LINC02315" "LINC02356" "RP11-499F3.2"
## [29] "RP1-158P9.2" "RP11-876N24.2" "RP11-60A24.3" "KLF2-DT"
## [33] "CH507-528H12.1" "RP11-114N1.1" "RP11-301F14.1" "CTD-2201E18.6"
## [37] "RP11-4D11.1"
## [1] 20
## [1] "RRAGD" "CALCRL" "SIDT1" "WSCD2"
## [5] "SLC8A3" "PLCB4" "GDAP1L1" "SLC24A4"
## [9] "ADAMTS9" "GUCY1A1" "GFRA2" "DELEC1"
## [13] "CYP4F12" "CYP4F3" "INSYN2B" "RP11-344B5.2"
## [17] "LINC01630" "LINC01768" "LINC00326" "DIRC3-AS1"
## [21] "AC007563.5" "RP11-154H17.1" "LINC02814" "SOCS2-AS1"
## [25] "RP11-1252I4.2" "RP11-124B13.1" "RP11-708B6.2" "LINC02327"
## [29] "FRMD6-AS2" "MAPT-AS1" "RP11-354K4.2" "RP11-323P17.2"
## [33] "LINC00836" "CTC-490G23.6" "RP11-492O8.3" "RP11-259G3.1"
## [37] "RP11-154D6.3" "RP11-609L3.3" "RP1-20N4.2" "RP11-423B13.1"
## [1] 21
## [1] "GABRE" "FAXC" "HESX1" "PBX3" "GTF2IRD1" "PLEKHA5"
## [7] "ATP2B4" "PDE4A" "CERS4" "MYO9B" "PALM" "ARHGEF18"
## [13] "PLIN3" "ZMIZ1" "CCND3" "NFIC" "ITPKB" "CTDSPL"
## [19] "ABCB9" "AKAP6" "JAZF1" "CLSTN2" "ADCY9" "PKNOX2"
## [25] "DHRSX" "PTPN9" "NPAS2" "KCND3" "PACS1" "CMTM4"
## [31] "OSBP2" "RILPL1" "PARVA" "LIME1" "NEAT1" "CUX1"
## [37] "FBXO17"
## [1] 22
## [1] "UPP2" "EPHA6" "CABLES1" "RERG"
## [5] "C4orf19" "MN1" "RNF150" "SLC24A3"
## [9] "HDHD5-AS1" "GRM3" "AC074391.1" "AP001628.6"
## [13] "SOX21-AS1" "AP000282.2" "RP11-498J9.2" "RPL34-DT"
## [17] "RP11-142A5.1" "LINC00886" "RP11-11N9.4" "LINC02234"
## [21] "CTC-329D1.2" "HS3ST5" "RP11-130F10.1" "F11-AS1"
## [25] "LINC01301" "RP1-84O15.2" "RP11-317N12.1" "RP11-431M3.1"
## [29] "RP11-526N18.1" "CTD-2349P21.11" "LINC01727" "RP11-281A20.2"
## [33] "RP11-437L7.2" "RP11-1289C17.1" "RP11-346I3.7" "EBF4"
## [37] "OLFM2"
## [1] 23
## [1] "GBE1" "SCLT1" "CMSS1" "CNTN1" "SAMD4A" "DGKG"
## [7] "KIF3C" "PCSK5" "GAB1" "TPD52L1" "WLS" "FOXO3"
## [13] "PDZRN3" "PALLD" "CEP350" "TNS3" "BCAS3" "FAM171A1"
## [19] "ZEB1" "FOXO1" "CACNB2" "ZNF608" "PCDH7" "ZFPM2"
## [25] "GNG7" "NCKAP5" "RGMA" "CADM1" "IRS2" "TPCN1"
## [31] "HRH1" "ZNF785" "PLCG2" "DNM3" "TOX"
## [1] 24
## [1] "NID1" "MOGAT1" "MTERF1" "TMEM241"
## [5] "MFSD4B" "SUGCT" "DLEU1" "DIO2"
## [9] "HEPN1" "RP1-292B18.4" "RP11-131L23.1" "MRPS9-AS2"
## [13] "TMLHE-AS1" "LINC01266" "PLCG1-AS1" "HDAC2-AS2"
## [17] "RP4-613B23.1" "GNA14-AS1" "GNG12-AS1" "LINC00513"
## [21] "LINC01937" "GS1-433O24.1" "PKN2-AS1" "ZBTB20-AS5"
## [25] "RORA-AS1" "MEF2C-AS2" "LIX1-AS1" "RP11-804N13.1"
## [29] "AP000462.2" "RP11-315E17.1" "RP11-39M21.1" "TSIX"
## [33] "RP11-470M1.2" "RP11-57G22.3" "RP11-793H13.14" "RP11-341N18.1"
## [37] "RP11-399K19.1"
## [1] 25
## [1] "ANOS1" "MAOB" "SEMA3A" "TRPM3" "MROH8" "SCG3"
## [7] "DHRS7B" "SLC1A2" "LAMA4" "TACR1" "DNAH7" "ENOX1"
## [13] "GTDC1" "TMEM108" "BEND6" "C10orf90" "WIF1" "IGFBP7"
## [19] "TSPAN5" "RGS7" "IMMP2L" "ROR1" "KLHL32" "VKORC1L1"
## [25] "ATP1A2" "ARHGAP31" "TBC1D1" "SEMA3C" "PHACTR3" "ZBTB16"
## [31] "C1orf21" "RIN2" "SHROOM3" "SEMA3D" "ENOX2" "SRGAP1"
## [37] "EFCAB2"
## [1] 26
## [1] "FILIP1L" "GLIPR1L1" "SEPTIN1" "AC002463.3"
## [5] "RP11-547I7.1" "ST7-AS2" "AC105461.1" "AC017101.10"
## [9] "CCDC192" "RP11-417B4.2" "RP11-46O21.2" "GRM3-AS1"
## [13] "PCDH9-AS4" "RP11-666F17.1" "RP11-109I13.2" "STARD13-AS"
## [17] "LINC02652" "LINC00960" "RP11-768G7.3" "GK-AS1"
## [21] "RP11-115N4.1" "RP11-274H2.2" "ANK2-AS1" "MAPK10-AS1"
## [25] "RP11-39E3.3" "RP11-351A11.1" "CTD-3239E11.2" "RP11-452H21.1"
## [29] "RP11-463D19.1" "RP11-513G19.1" "A2ML1-AS1" "RP11-887P2.5"
## [33] "PRKCA-AS1" "RP11-138H11.1" "LINC01374" "RP11-576O3.1"
## [37] "RP11-394G3.3" "RP11-555K12.4"
## [1] 27
## [1] "ATP11A" "PDE8B" "KCTD1" "ARRDC4"
## [5] "SPOCK1" "LMOD1" "ADAP2" "SHISA6"
## [9] "CTA-292E10.6" "LMCD1-AS1" "OSMR-AS1" "MALAT1"
## [13] "RP11-175O15.1" "ADGRL1" "TRHDE" "RFX2"
## [17] "DAAM1" "CDH20" "UNC5B" "RFX4"
## [21] "ADGRB3" "ENSA" "DENND2A" "FLCN"
## [25] "NAV2" "MOB3A" "CADM2" "SPACA6"
## [29] "MAML2" "KIF9-AS1" "AC004951.6" "LINC00342"
## [33] "HMGA1P4" "RP3-414A15.10" "RP11-35G9.5" "ATP6V0D1-DT"
## [37] "RP11-514P8.10"
## [1] 28
## [1] "PPEF1" "EPB41L4B" "GALNT16" "FRK" "EYA4" "SIPA1L2"
## [7] "APOC1" "EPSTI1" "AXDND1" "EPHX4" "SYN1" "DCN"
## [13] "RRP12" "RIMBP2" "ABCA7" "ATP2B3" "PPP1R15A" "CASS4"
## [19] "KAT8" "ISYNA1" "EPHB6" "CLNK" "PPFIBP1" "CHD5"
## [25] "DUSP1" "CDKN1A" "MICAL1" "BIN1" "SLC43A1" "DOC2A"
## [31] "CACNB3" "DUSP8" "HAUS7"
## [1] 29
## [1] "TACC2" "SNHG31" "COL23A1" "RARB"
## [5] "SESN1" "GRK3" "CAB39L" "MPP6"
## [9] "LIN7A" "PACRG" "ARSB" "SEM1"
## [13] "IQCA1" "ARHGAP29" "GLTP" "CLVS2"
## [17] "C2CD2" "NRG2" "ADORA1" "CKB"
## [21] "PDE3A" "CALCB" "ANO6" "PPP1R42"
## [25] "CCDC30" "KBTBD12" "NKAIN2" "ZNF358"
## [29] "LYRM4" "LINC00598" "WARS2-AS1" "DLEU2"
## [33] "LINC01135" "RP11-507B12.1" "RP11-379B18.8" "RP11-358F13.1"
## [37] "RP11-166M16.1"
## [1] 30
## [1] "CD38" "HHAT" "ARHGAP28" "ANKRD24"
## [5] "ZFR2" "KIAA1549L" "PEX5L" "DNAH6"
## [9] "TFAP2E" "TRIM22" "PEBP4" "PLXNC1"
## [13] "DNAAF1" "KIF6" "JAM3" "VWA3B"
## [17] "GRIK1" "ZBTB44-DT" "CIITA" "PCED1B"
## [21] "PRELID2" "SLC4A5" "MAML3" "RP1-167A14.2"
## [25] "TARID" "AF131217.1" "LINC01725" "LINC00407"
## [29] "DRAIC" "RP4-785G19.5" "LINC00958" "RP11-396B14.2"
## [33] "RP1-41C23.1" "RP11-239A17.1" "RP11-274G22.1" "RP11-125D12.3"
## [37] "RP11-373E16.6" "RP11-255O19.2" "ARHGEF3" "LINC01094"
## [1] 31
## [1] "BNC2" "MCUB" "VCAN" "ARHGAP6"
## [5] "KITLG" "ST6GALNAC2" "ST6GAL1" "CCL2"
## [9] "JHY" "PRRX1" "SOHLH2" "LRAT"
## [13] "ST18" "CCDC175" "SAMD3" "SLITRK5"
## [17] "FBN1" "TEKT1" "HTR1E" "RCAN2"
## [21] "CAVIN1" "PLCXD3" "CHST6" "CCK"
## [25] "SAMD11" "PLPP4" "AP001347.6" "RP1-187B23.1"
## [29] "RP11-146I2.1" "AL163953.3" "LINC01088" "CTB-35F21.1"
## [33] "LINC00609" "RP1-79C4.4" "RP11-403A3.2" "RP5-1015P16.1"
## [37] "RP11-6L16.1"
## [1] 32
## [1] "AHRR" "POLR2I" "CA1" "LRTM1"
## [5] "AGBL3" "ABI3BP" "BTG2" "LINC01931"
## [9] "SHOC1" "CLMP" "PAPPA" "CARNMT1-AS1"
## [13] "ANKUB1" "Z83001.1" "ASTN2-AS1" "RP1-232L24.3"
## [17] "AC009501.4" "AC037445.1" "RP5-1101C3.1" "CTD-2015H6.3"
## [21] "RP11-223C24.1" "RP11-348J24.1" "RP11-517I3.1" "ZFPM2-AS1"
## [25] "RP11-649G15.2" "BBOX1-AS1" "CTD-2537O9.1" "RP11-1H15.2"
## [29] "RP11-144F15.1" "RP11-370I10.2" "RP11-184D12.1" "RP11-58G13.1"
## [33] "CTC-513N18.6" "CH17-140K24.2" "BCL6-AS1" "RP11-592G13.2"
## [37] "NUP210L"
## [1] 33
## [1] "TENT5A" "UNC79" "PKIB" "ST6GAL2"
## [5] "HHIP" "P2RY14" "RFLNA" "PNMA3"
## [9] "NAP1L3" "FSIP2" "CLDN4" "RP11-306O13.1"
## [13] "LCNL1" "LINC02649" "AC072062.3" "PCDH9-AS2"
## [17] "GPC5-AS2" "LINC02250" "AC008067.2" "RP13-143G15.4"
## [21] "RP11-657O9.1" "LRP4-AS1" "C1QTNF7-AS1" "LINC01950"
## [25] "RP11-116O11.1" "AP000487.6" "RP11-20E24.1" "PRANCR"
## [29] "RP11-72M17.1" "HIF1A-AS3" "LINC01572" "PSMD7-DT"
## [33] "CTD-2282P23.2" "RP11-221G19.1" "RP11-69G16.2" "RP11-314E10.1"
## [1] 34
## [1] "MAMLD1" "BID" "GAB2" "MYO16"
## [5] "PPM1H" "DPYSL3" "EEPD1" "ABCC4"
## [9] "FAM117B" "TMEM132B" "STOX2" "LIPE-AS1"
## [13] "APTR" "TENM3" "AQP1" "MRPL33"
## [17] "RP11-410D17.2" "MGAM" "RASAL2" "HSD17B14"
## [21] "MAST3" "BNIP3L" "UBE2R2" "SH3PXD2A"
## [25] "CCDC146" "ARHGAP26" "MAGI1" "TIAM1"
## [29] "DHRS3" "PLEKHA7" "GNG4" "SLC35E3"
## [33] "ABAT" "ANKS1B" "MAPT"
## [1] 35
## [1] "TENM1" "MRC2" "CCDC85A" "NTN1" "RIPK2" "RASD1"
## [7] "NT5DC3" "RGS4" "ID1" "TMEM160" "TRIM5" "CHI3L1"
## [13] "BEX1" "TESPA1" "RNF165" "LYPD6B" "ARHGAP27" "CCDC141"
## [19] "FABP5" "PRTG" "SCG5" "VWCE" "GINS3" "STAC3"
## [25] "IL1RAPL2" "SVIL" "KCNMB2" "BAALC-AS2" "LRRC24" "FGF17"
## [31] "SPSB1" "YOD1" "FAM110C"
## [1] 36
## [1] "RP11-436D23.1" "COL5A3" "LAMB4"
## [4] "LRMDA" "FREM2" "KCNE4"
## [7] "TDRD9" "RANBP3L" "CSDC2"
## [10] "TRDN" "ZNF98" "LINC01208"
## [13] "ARL17B" "SPRY4-AS1" "PDYN-AS1"
## [16] "KCNMB2-AS1" "MEIKIN" "ETV5"
## [19] "KCNK15-AS1" "TMEM161B-AS1" "RP11-446J8.1"
## [22] "RP11-346L1.2" "MTRNR2L1" "RP11-328J6.1"
## [25] "RPPH1_ENSG00000259001" "TAPT1-AS1" "MAFG-DT"
## [28] "RP11-838N2.5" "MTRNR2L12" "RP11-711K1.8"
## [31] "CH507-513H4.1" "LINC02246" "RP1-166D18.1"
## [34] "RP11-398J12.1"
## [1] 37
## [1] "LIX1" "LINC00637" "TLE2" "PDZD4"
## [5] "P2RX7" "SEC14L5" "SPAG1" "AGFG2"
## [9] "USP9Y" "MOB3B" "PATJ" "DGKB"
## [13] "KCNH5" "DOCK11" "CNKSR2" "PARP8"
## [17] "DEPTOR" "ADCY8" "ZNF653" "ADCY1"
## [21] "CFAP47" "NLGN4Y" "ARMC3" "SLC38A11"
## [25] "TTTY14" "UTY" "CFAP54" "DISP3"
## [29] "XXbac-BPG55C20.7" "TTTY10" "LINC00278" "LINC00884"
## [33] "CTD-2643I7.5" "MIR4300HG" "CTD-2054N24.2" "RP11-93B21.2"
## [37] "RP11-125C10.1"
## [1] 38
## [1] "SNCAIP" "BICC1" "MT2A" "KIAA1328"
## [5] "STPG2" "MT1E" "DPP10" "ADD3-AS1"
## [9] "AC026188.1" "LNC-LBCS" "CCDC26" "LINC02884"
## [13] "RP1-45C12.1" "MMADHC-DT" "RP11-120D5.1" "RP11-195C7.1"
## [17] "SOX2-OT" "MAILR" "RP11-266O8.1" "RP11-739G5.1"
## [21] "RP11-157E16.1" "RP11-561I11.4" "RP11-378A12.1" "RP11-589M4.5"
## [25] "RP11-574F11.4" "RNF19A" "CTNNA2" "ST8SIA1"
## [29] "HIF3A" "ARHGEF4" "KCNN3" "NCAM2"
## [33] "ZNF704" "PHYHD1" "APOLD1" "ZFP36L1"
## [37] "RP11-799O21.2"
## [1] 39
## [1] "PRKCQ" "SLC16A6" "WNT5B" "HS3ST3B1"
## [5] "GPNMB" "FHDC1" "IFI44L" "FHAD1"
## [9] "NTNG1" "C4orf45" "SNX31" "RAB39A"
## [13] "RFX8" "SULT1A2" "AC007277.3" "SNAP25-AS1"
## [17] "KIF5C-AS1" "AC009264.1" "NPIPB2" "CDKN2B-AS1"
## [21] "LEFTY1" "C5orf17" "RP11-745L13.2" "MTRNR2L8"
## [25] "DISC1FP1" "RP11-397A16.1" "APP-DT" "RP11-413N10.3"
## [29] "RP11-364P22.4" "CTD-2040G12.2" "AC006296.4" "RP11-520F22.1"
## [1] 40
## [1] "CCDC80" "SLC26A8" "LRRC9" "WDR64"
## [5] "CD200R1" "IPO9-AS1" "RP11-132E11.2" "AC092684.1"
## [9] "LINC01877" "SEMA6A-AS1" "NEUROG2-AS1" "VCAN-AS1"
## [13] "STPG2-AS1" "CENATAC-DT" "RP11-116N8.1" "RP11-104E19.1"
## [17] "PTCSC3" "CRIM1-DT" "RP11-793A3.2" "LINC00842"
## [21] "RP5-847G17.1" "CTD-2172F7.1" "SLCO1A2" "KLHL4"
## [25] "DNAH11" "BEST3" "HNMT" "ANGPT1"
## [29] "COX7A1" "C2" "METTL7B" "AC092155.4"
## [33] "RP1-111D6.3" "RP5-1198O20.4" "RP11-469A15.2" "RP11-90C4.1"
## [37] "LINC02251" "RP11-259K15.2" "RP11-627D16.1" "RP11-542F9.2"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_1"
## [1] "PRKAR2B" "NRXN3" "ELAVL2" "MMP16" "CADPS"
## [6] "CCSER1" "SYT1" "MAP2" "RBFOX1" "PDE1A"
## [11] "RIMS3" "DPP6" "LRRC4B" "SNTG1" "CACNA1B"
## [16] "RBFOX3" "GRM5" "NLGN1" "FRMPD4" "DLGAP1"
## [21] "ARPP21" "CNTNAP2" "RIMS2" "CSMD1" "OPCML"
## [26] "KCNH7" "RALYL" "SYN3" "KCNIP4" "ELAVL3"
## [31] "RYR2" "MEG3" "RP1-30E17.2" "IQCJ-SCHIP1"
## $reactome
## category over_represented_pvalue
## 596 neuronal system 5.219000e-07
## 725 protein protein interactions at synapses 1.386388e-05
## 595 neurexins and neuroligins 5.354203e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 596 1.0000000 10 72 0.0005860937
## 725 0.9999994 6 25 0.0077845699
## 595 0.9999977 5 18 0.0200425653
##
## $go_bp
## category over_represented_pvalue
## 2093 neurotransmitter secretion 5.076878e-06
## 3767 regulation of synaptic vesicle exocytosis 1.013222e-05
## 4266 synaptic vesicle exocytosis 1.585970e-05
## 2094 neurotransmitter transport 2.795121e-05
## 4455 vesicle mediated transport in synapse 4.030425e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 2093 0.9999998 6 22 0.02274683
## 3767 0.9999999 4 6 0.02274683
## 4266 0.9999994 5 16 0.02373668
## 2094 0.9999983 6 29 0.03137523
## 4455 0.9999974 6 29 0.03619322
##
## [1] "set_14"
## [1] "CPED1" "SPATA6L" "F3" "SLC14A1"
## [5] "SLC44A3" "SLC22A3" "SLC43A2" "FTH1"
## [9] "ERICH3" "CCBE1" "WNT7B" "MAMDC2-AS1"
## [13] "MALRD1" "SOX1-OT" "CHL1-AS2" "PPP1R26-AS1"
## [17] "XIST" "OBI1-AS1" "LINC01934" "RP11-390F4.6"
## [21] "SUCLG2-AS1" "BAALC-AS1" "LINC01182" "LINC00923"
## [25] "LINC00499" "GS1-57L11.1" "RP11-156K13.1" "RMST"
## [29] "RP11-798K3.2" "AC007193.6" "RP11-496B10.6" "RP11-382N13.7"
## [33] "RP11-563M4.2"
## $reactome
## category
## 1086 transport of bile salts and organic acids metal ions and amine compounds
## 965 slc mediated transmembrane transport
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1086 2.525065e-05 0.9999998 3 9
## 965 6.625814e-05 0.9999986 4 32
## FDR
## 1086 0.02835648
## 965 0.03720395Session information
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8954950 478.3 16112782 860.6 NA 15573326 831.8
## Vcells 16664148 127.2 31261907 238.6 65536 31261907 238.6## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] goseq_1.50.0 geneLenDataBase_1.34.0 BiasedUrn_2.0.10
## [4] fgsea_1.24.0 biomaRt_2.54.1 limma_3.54.2
## [7] tidyr_1.3.0 ggpubr_0.6.0 ggplot2_3.4.2
## [10] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 GenomeInfoDb_1.34.9
## [9] tools_4.2.3 backports_1.4.1
## [11] bslib_0.4.2 utf8_1.2.3
## [13] R6_2.5.1 mgcv_1.8-42
## [15] DBI_1.1.3 BiocGenerics_0.44.0
## [17] colorspace_2.1-0 withr_2.5.0
## [19] tidyselect_1.2.0 prettyunits_1.1.1
## [21] bit_4.0.5 curl_5.0.1
## [23] compiler_4.2.3 cli_3.6.1
## [25] Biobase_2.58.0 xml2_1.3.4
## [27] DelayedArray_0.24.0 rtracklayer_1.58.0
## [29] sass_0.4.5 scales_1.2.1
## [31] rappdirs_0.3.3 Rsamtools_2.14.0
## [33] stringr_1.5.0 digest_0.6.31
## [35] rmarkdown_2.21 XVector_0.38.0
## [37] pkgconfig_2.0.3 htmltools_0.5.5
## [39] MatrixGenerics_1.10.0 dbplyr_2.3.2
## [41] fastmap_1.1.1 rlang_1.1.0
## [43] rstudioapi_0.14 RSQLite_2.3.1
## [45] BiocIO_1.8.0 jquerylib_0.1.4
## [47] generics_0.1.3 jsonlite_1.8.4
## [49] BiocParallel_1.32.6 dplyr_1.1.2
## [51] car_3.1-2 RCurl_1.98-1.12
## [53] magrittr_2.0.3 GO.db_3.16.0
## [55] GenomeInfoDbData_1.2.9 Matrix_1.6-4
## [57] Rcpp_1.0.10 munsell_0.5.0
## [59] S4Vectors_0.36.2 fansi_1.0.4
## [61] abind_1.4-5 lifecycle_1.0.3
## [63] stringi_1.7.12 yaml_2.3.7
## [65] carData_3.0-5 SummarizedExperiment_1.28.0
## [67] zlibbioc_1.44.0 org.Hs.eg.db_3.16.0
## [69] BiocFileCache_2.6.1 grid_4.2.3
## [71] blob_1.2.4 parallel_4.2.3
## [73] crayon_1.5.2 lattice_0.20-45
## [75] splines_4.2.3 Biostrings_2.66.0
## [77] cowplot_1.1.1 GenomicFeatures_1.50.4
## [79] hms_1.1.3 KEGGREST_1.38.0
## [81] knitr_1.44 pillar_1.9.0
## [83] GenomicRanges_1.50.2 rjson_0.2.21
## [85] ggsignif_0.6.4 codetools_0.2-19
## [87] stats4_4.2.3 fastmatch_1.1-3
## [89] XML_3.99-0.14 glue_1.6.2
## [91] evaluate_0.20 png_0.1-8
## [93] vctrs_0.6.2 gtable_0.3.3
## [95] purrr_1.0.1 cachem_1.0.7
## [97] xfun_0.39 broom_1.0.4
## [99] restfulr_0.0.15 rstatix_0.7.2
## [101] tibble_3.2.1 GenomicAlignments_1.34.1
## [103] AnnotationDbi_1.60.2 memoise_2.0.1
## [105] IRanges_2.32.0